view reorient_coordinates.xml @ 1:a0e05808610a default tip

Uploaded

<tool id="reorient_coordinates" name="Reorient Coordinates" version="0.1.0">
  <description>Switches Start and End if needed</description>

  <command interpreter="perl">reorient_coordinates.pl $input_file $output_file</command>
  
  <inputs>
      <param name="input_file" type="data" format="tabular" label="3-column tabular file with columns 2 and 3 indicating genomic positions"/>             
   </inputs>
   
  <outputs>
    <data name="output_file" format="tabular" />
  </outputs>
       
<!-- TODO implement tests: namely generate test data and put it in place     
  	<tests>
		<test>
			<param name="input_file" value="test_transcript_count.bam" />
			<param name="coherent" value="1" />
			<output name="output_file" file="test_transcript_count.tab" />
		</test>
	</tests>        
-->       
    <help>
    
Switches positions in a tabular file to guarantee that the 2nd colum is always less or the same as the 3rd column.

E.g.
datafile:
entry1	100	200
entry2	200	200
entry3	300	200

Output:
entry1	100	200
entry2	200	200
entry3	200	300

------

**Citation**

This tools and Galaxy wrapper was developed by the IGC Bioinformatics unit (author: Daniel Sobral [e-mail])

  </help>

  </tool>